Cufflinks 2.2.0 installation issue

[shocker8786]

I want to use the new cuffquant and cuffnorm features of cufflinks 2.2.0, so I removed my 2.1.1 version of cufflinks and downloaded the source code for version 2.2.0. However, after installation, I go to the install directory and type cuffquant to run the program, but I get the following message:

cuffquant: command not found

This happens even though I can see the cuffquant module is there. If I try and run cufflinks, or one of the other modules that was available in the old version, it runs fine, but the version is listed as 2.1.1. I'm working on a linux, so I tried downloading the binaries, and I have the same issue. Has anyone else has this problem? It seems to me that there is something wrong with the release, but I have not received a response back from the cufflinks authors or the google group forum. Thanks for looking.

[GenoMax]

Is the execute bit set on the new cuffquant (v.2.2.0) file? If not that should be an easy fix ($ chmod u+x /path_to/cuffquant)?

We installed cufflinks 2.2.0 last week and cuffquant in that install is executable.

[Bukowski]

It sounds very much like you haven't actually uninstalled your original cufflinks installation

"which cufflinks"

should show you which binary you're executing when you run the command. Is this the path you expected to find it on?

Having a look at your $PATH "echo $PATH" will tell you where your shell environment will actually look for binaries.

If your 2.2.0 cufflinks binaries are in none of these folders, 'cuffquant' will do nothing at all.

[bio_boris]

You don't necessarily need to compile it from source. Just get the frozen binaries

wget http://cufflinks.cbcb.umd.edu/downlo..._x86_64.tar.gz
tar xvf cufflinks-2.2.0.Linux_x86_64.tar.gz
cd cufflinks-2.2.0.Linux_x86_64
./cuffquant